Althoughin vitrostudies have been invaluable in revealing the complex biochemistry of the blood coagulation system, meaningfulin vivostudies of thrombogenic mechanisms have previously been hindered by the absence of suitable assays. This article reviews the recent development and/or contemporary clinical application of plasma-based immunoassays for coagulation markers (factor XIIa, factor IX activation peptide, prothrombin fragment F1 + 2, thrombin-antithrombin complex and fibrinopeptide A) and for the fibrinolytic marker, D-dimer, which have enabled a critical re-appraisal of some long-standing hypotheses. In chronic renal disease the intrinsic coagulation pathway was found to be activated before haemodialysis and increased end-stage coagulation activity was detected during dialysis when heparization was limiting. No evidence was found to support the generally accepted hypothesis that thrombogenesis in dialysis is triggered by stimulation of the contact system following exposure of blood to the dialyser membrane. Instead, it is postulated that it is a failure of regulation of end-stage coagulation proteinases (owing to the absence of endothelium) which is responsible for increased thrombogenesis in the dialyser circuit. Excessive end-stage coagulation activity was observed during cardiopulmonary bypass (CPB) surgery and in patients undergoing general thoracic surgery. The data did not accord with the hypothesis that the contact system provides the major thrombogenic trigger in CPB surgery. It is proposed that, in general thoracic surgery, a powerful procoagulant stimulus is provided via the tissue factor-factor VIIa pathway and that the same mechanism is also primarily responsible for triggering thrombogenesis during CPB surgery. The established hypothesis of a prethrombotic state in hereditary AT III deficiency is challenged by the inability to detect increased coagulation activity in asymptomatic At III deficient patients. It is concluded that the AT III concentration in deficient members is sufficient to enable regulation of the coagulation system in the basal state, whereas failure to regulate the coagulation system only occurs following a major procoagulant stimulus, which overwhelms the impaired inhibitory capacity and triggers thrombosis. These findings highlight the advantages of using plasma-based immunoassays to investigate thrombogenic mechanisms in hypercoagulable states and have important implications for the further study and treatment of blood-surface interactions and thrombotic disease.